sample2markers.py failed at samtools sort

[Jamie Kwok]

Hello,

When I run this command:
sample2markers.py --verbose --ifn_samples strainphlan2_output/15V0257194_after_human_F2.sam.bz2 --input_type sam --output_dir ./test2

It returns this error:
[bam_sort_core] fail to open './test2/15V0257194_after_human_F2.sam.bz2.bam.sorted': No such file or directory
(...trimmed for clarity)
ooSubprocessException: Failed when executing the command: dump_file.py --input_file strainphlan2_output/15V0257194_after_human_F2.sam.bz2 | samtools view -bS - | samtools sort -o - ./test2/15V0257194_after_human_F2.sam.bz2.bam.sorted
return code: 1

I guess it failed at samtools sort. I don't understand why it's '-o -' since -o is specifying the output file which should be /test2/15V0257194_after_human_F2.sam.bz2.bam.sorted. Why is the stdin '-' in between? I am confused because other people have seemed to run it smoothly. Please help. Thank you very much.

Best regards,
Jamie

[Duy Tin Truong]

Hi Jamie,

Can you try to run the above command alone to see what is the problem?

dump_file.py --input_file strainphlan2_output/15V0257194_after_human_F2.sam.bz2 | samtools view -bS - | samtools sort -o - ./test2/15V0257194_after_human_F2.sam.bz2.bam.sorted

In addition, can you check if all dependencies were installed with the correct version as in the tutorial, especially samtools 0.1.19?

Cheers,

Tin

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[Jamie Kwok]

Hi Tin,

Thank you very much for your reply. I originally have samtools 1.3.1, and after changing to 0.1.19, and fixing a typo (test/ instead of test2), it seems to go farther:

$ dump_file.py --input_file strainphlan2_output/15V0257194_after_human_F2.sam.bz2 | samtools view -bS - | samtools sort -o - ./test/15V0257194_after_human_F2.sam.bz2.bam.sorted | samtools mpileup -u - | bcftools view -c -g -p 1.1 - | fix_AF1.py --input_file - | vcfutils.pl vcf2fq

[bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] EOF marker is absent. The input is probably truncated.

Error: Could not parse --min-ac -g

@

Use of uninitialized value $l in numeric lt (<) at /home/jamie/bcftools-1.3.1/vcfutils.pl line 566.

+

Use of uninitialized value $l in numeric lt (<) at /home/jamie/bcftools-1.3.1/vcfutils.pl line 566.

[samopen] SAM header is present: 1036027 sequences.

[mpileup] 1 samples in 1 input files

However there is no final output?

I checked that the 15V0257194_after_human_F2.sam.bz2 is non-empty.

Best regards,

Jamie

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[Duy Tin Truong]

You should use bcftools 0.1.19 as well.

Cheers,

Tin

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[Jamie Kwok]

Thank you so much Tin! (and silly me!) It works now.

Best regards,

Jamie

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